Baking to an image using cycles with two sets of existing uvs
For Cycles baking, the Vector input of the texture being baked to has no effect(for now).  You must select the bake target UV's using the following dialogue.

 

It's one of those controversial design decisions but I do believe that python can access this input socket so scripters can programmatically choose the UV Coordinates.  I have not tried this though so I could be totally wrong about how that works.